The Bantu völkerwanderung

Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an accretion of a non-Anglo-Saxon stream of immigrants who serial adopted the Anglo culture, more or less. Sometimes this co-option of Anglo-Saxon norms may surprise. “Black English” (i.e., Ebonics) actually seems to be a genetic descendant of lower class northern English dialects. Other distinctive components of black American (e.g., “jumping the broom“) culture can also plausibly be derived back to the British Isles.

So cultural change is in the “its complicated” segment of dynamics. We have to go on a case-by-case basis. For the Bantu expansion though we have a good answer now thanks to genetics: this cultural change almost certainly was accompanied by a massive demographic migration. Thanks to Brenna Henn and company you can even run some analyses on your desktop to confirm the reality of this model. I pulled down the 55,000 SNPs from various African populations, merged with Palestinians, Tuscans, and Maya as outgroups, and pruned down to ~40,000 after removing those which were missing in more than 1% of the cases. The Hadza are also gone, as they’re such a small isolated group who always hogged up K’s all by themselves. I ran a bunch of different ADMIXTURES, from K = 2 to 12. You can see all 12 here, but let’s just focus on the 12th.

Below is a bar plot, somewhat sorted by ADMIXTURE elements. I’ve reedited some of the labels for clarity, adding regions. I’m sure some of you are ignorant of where the Brong people (Ghana) are from as I was before I looked them up. Also, please be careful about ADMIXTURE. There is a “Fulani” ancestral component below, but I’m 90% sure that’s just an artifact of recent Fulani demograhics + their unique genetic admixture.

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The New York Times "pay wall"

So what do readers of this blog think? Pay or no pay? It’s useful, and The New York Times is pretty massive in scope, if sometimes lacking in breadth. I love their data-oriented stuff, but I ignore their columnists and a lot of their “analysis,” which is frankly substandard if I know anything about the topic (which suggests to me if I don’t know about the topic, they barely do too). There are certain areas where blogs have a comparative advantage, and I don’t see why an organization with other strengths would even make an attempt.

Personal genomics gets very personal

Dan MacArthur points me to this nice post over at Daily Kos, Our Genome Decoded: How Companies Like 23andMe Are Advancing the Field of Personal Genomics:

…However, in the past few years several private biotech companies have started offering a “personal genome service” that involves sequencing the most variable portions of our DNA. The goals are straightforward – to give individuals information about their ancestry and inherited traits. While there are definite limitations – both technically and bioethically – to the amount and type of information that can be obtained from personal genome sequencing, in my case the service answered a lingering question about something important to me, and thus was well worth it.

In this article, I’m going to tell the story about why I chose to purchase a personal genome service, briefly explain how it works, show my interesting results, and finally, provide some commentary on how these services will impact the fields of genomics and medicine.

One step at a time. I also appreciate that Michelle keeps posting on her ADMIXTURE results.

Bravo for Mormons!

Trying to Relish the Big Time, Even When It Brings a Cringe:

The house lights came up and it was intermission at “The Book of Mormon,” the new Broadway musical about a pair of innocent young Mormon missionaries sent to Uganda to spread the faith. John Dehlin, a graduate student who flew in from Utah to see the show with a group of Mormons from around the country, was still riveted to his theater seat, having flashbacks.

“It’s way, way too close to home,” he said, recalling his own missionary years in Guatemala: the shock at the poverty and violence, the pressure from the mission president to baptize more natives, the despair when his mission companion ran off with a local girl — and the Mormon mandate, above all, to repress doubt and remain relentlessly cheery.

A friend in the crowded theater aisle, Paul Jones, passed by and gave Mr. Dehlin a high-five and a hug. “It’s right on,” said Dr. Jones, a dentist from Gilbert, Ariz., “but I cringed a little bit, a couple of times.”

The arrival of a Broadway musical that ridicules their religion, produced by the creators of the scathingly satirical television show “South Park,” is proving to be a cringe-worthy moment for many Mormons.

And yet, even though the very name of the show appropriates the title of the church’s sacred scripture, there have been no pickets or boycotts, no outraged news releases by Mormon defenders and no lawsuits.

This is intentional. Mormons want people to know that they can take it.

Not all religious communities react in the same way. In Birmingham, England, 2004, Theatre attacks Sikh play protest:

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The end of Ayla & The Land of Painted Caves

I read  Jean Auel’s Clan of the Cave Bear in elementary school at a friend’s house during a sleep over. It was next to the bedside, and I decided to pick it up. I’d thought it was a human evolution book from the cover. I read  2/3 of the book by dawn, took a few hours to catch up on sleep, and then finished the rest before the afternoon. I read almost no fiction outside of what was assigned in school as a child, but this was the exception (I also read a lot of Greek mythology, though I’m not sure that counts). The three sequels I finished in middle school when I noticed there were sequels! By the time book 5, Shelter of the Stones, came out in the early aughts I’d lost interest. I’ve moved on, but many have not. The last book, The Land of Painted Caves, is now out. The Los Angeles Times has written a retrospective of the series.

Since Amazon has a 1 to 5 star rating system, I thought I’d plot the results for the first five books. On the y-axis you have the number who gave a particular star value to a given book (the order of the books goes from left to right, book 1 to book 5). I haven’t read Shelter of the Stones, but I agree with the median reviewers on Amazon that The Mammoth Hunters was the most uninteresting of the first four books.

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The day of the farmer

About five months ago I read Peter Bellwood’s First Farmers: The Origins of Agricultural Societies. Bellwood’s thesis is simple: that the first adopters of farming entered into a period of rapid demographic expansion and by and large replaced non-farming groups. The populations which dominate the world today in this model are then the descendants of the very small set of cultures which ~10,000 years ago triggered the Neolithic Revolution. When Bellwood presented his thesis in the mid-2000s many would have dismissed it out of hand. Today I believe we have to take this model seriously.

There are two primary reasons from my perspective why I am now thinking about Bellwood’s thesis a great deal. First, the archaeogenetic inferences based on distributions of modern allele frequencies which suggested that the Neolithic Revolution in Europe was a matter of cultural diffusion seem far shakier. With such genetic models no longer taken for granted the recent historical, semi-historical, and ethnographic evidence, on farming transitions must be given much more weight. The case of the Bantu expansion in Africa seems to be semi-historical. The Bantu farmers themselves were not literate but their wave of advance was in historical time. Tellingly, the Bantu speaking populations of Southern Africa are genetically more similar to the Fang of Cameroon then they are to the Khoisan to their west! More well documented has been the attempts by Europeans to settle various lands overseas in their colonial adventures. They have been able to marginalize populations which did not habitually practice intensive agriculture relatively easily (note that the locus of Afrikaner settlement was initially around the Cape, where Bantu influence was minimal and Khoikhoi pastoralists were dominant). In contrast, in regions like Mesoamerica where obligate intensive agricultural civilization had deep roots there was no biological replacement, but hybridization.

An argument can be made that the initial farmers did not have so many advantages over their hunter-gatherer neighbors. So the power and force of the mass agricultural way of life which bore down upon the indigenes of Australia was qualitatively different because the Europeans who arrived were the outer wave of an ancient and ruthlessly efficient civilization of farmers, honed to brutal perfection through the cauldron of inter-group competition over thousands of years. I think the best counter argument against this is the evidence of rapid sweeps of cultural forms in European in prehistory, as well as rapidity of the success of the Bantu agricultural toolkit.

The new genome blogger Diogenes expresses the thesis of agricultural replacement to near maximal levels in the model which he is attempting to test with ADMIXTURE runs. Here are his propositions (formatting reedited for clarity):

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The excitement of clothed porn stars

Porn Stars, Clad? They Seem to Appeal to Indonesian Filmgoers:

Ms. Aoi, and others like her, are the secret of a winning formula stumbled upon by Maxima Pictures, the production house where Mr. Hidayat is an executive producer. For two years, Maxima has made some of Indonesia’s most popular domestic films based on a simple premise: that many in Muslim-majority Indonesia will pay to see foreign porn stars perform — clothed — in local films. Just don’t expect Indonesians to own up to it.

“We’re hypocrites,” said Mr. Hidayat, who is a Muslim. “People know who they are, but they won’t admit it. It’s a love-hate thing.”

This sort of “counter-intuitive” behavior makes total sense in light of the work reported in Paul Bloom’s How Pleasure Works: The New Science of Why We Like What We Like. People consume in a particular context. The hedonic experience can’t be isolated from its history and the prior facts (and expectations) you bring into it. This sort of insight is essential when we start talking about utilitarianism as if it’s a simple calculus.

The limits of computational power – shades of 1982

Two Steps Forward, Two Steps Back:

I got my daughter a netbook, so now my computer is doing Harappa Prohect work 24×7.

Also, Simranjit was nice enough to offer me the use of a server. For privacy reasons, I am not going to upload any of the participants’ data there but it is much faster than my machine and hence very useful for running Admixture on the reference data (especially with crossvalidation).

As for steps back, I downloaded the current 1000genomes data (1,212 samples, 2.4 million SNPs). It’s in vcf format. Using vcftools to convert it to ped format will take about 3 weeks. Yes you heard that right. BTW, the good stuff from a South Asian point of view will come later this year with a 100 Assamese AhomF, 100 Kayadtha from Calcutta, 100 Reddys from Hyderabad, 100 Maratha from Bombay and 100 Lahori Punjabis.

Also, I spent most of Sunday evening and night in the ER and got a diagnosis of ureterolithiasis for my efforts. All I can say is: Three cheers for Percocet!!

First, wish Zack well. Second, he has over 70 individuals in the Harappa Ancestry Project data base (in addition to the public data sets). If you’re South Asian, Iranian, Burmese, or Tibetan, here are the details of participation.

Genetic paternalists are very patronizing

An comment below on my post Genetic paternalism & the F.D.A.:

I came across your inflamed post from March 9th and the more I read the more disappointed I became, especially when I read your comment “following twitter, it seems there may be a distinction between raw sequence and interpretation. it may be the latter where there are “gatekeepers.” probably for reasons of liability, public safety, etc. (ergo, FDA). i see the logic, but from a perspective of utility i don’t think that the regs will improve human well being. though that’s probably not the implicit rationale behind “interested parties.””
The distinction there is ABSOLUTELY CRUCIAL. There is a huge difference between providing your raw genomic information, and providing diagnostic interpretation.

The AMA letter clearly stated that it was directed to ” direct to consumer (DTC) genetic tests that make medical claims” and it is “the making of medical claims” that puts certain offerings of DTC genetic testing squarely in the FDA’s domain; uninterpreted DTC genetic test results – the raw sequence – are NOT in the FDA’s domain under current regulations. Medical claims are. And I have not heard the FDA claim that they would even try to regulate uninterpreted DTC genetic test results. Have you? (not a rhetorical question)

I found your sloppy, over-emotional post — and the unthinking overreactions by commentors, to be deeply disheartening. How can people claim to be super-smart and bellow about their right to their own information and to be better informed than 99% of MDs (sheesh there is some unsubstantiated overstatement) — how can these people lack the basic common sense, much less decency, to read carefully and think through the actual regulatory issues, before starting to self-righteously holler about being stepped on? Shame on all of you who did that.

Razib – please post an “oops I over-reacted” with respect to this entire over-heated mess that you have poured oil onto. That would show some integrity and thoughtfulness, which we need more of. We do not need more emotional over-reactions to regulatory issues. The dietary supplement people are doing just fine with that.

Before entering into a presumptuous and patronizing lecture, it would have been nice to explicitly admit some conflict of interest here (some MDs arguing for control over this industry did in earlier comments). The IP originates from Joan and Sanford I. Weill Medical College and Graduate School of Medical Sciences of Cornell University. This is the internet. If you’re going to get stuffy and professorial you might want to use your real name.